如何计算大型 FASTA 文件中包含的序列的氨基酸组成百分比

Question

我想计算 FASTA 文件中单独包含的每个序列的氨基酸组成，但我很难做到这一点。我知道我可以使用下面的代码来完成，但这需要我分别输入每个序列，而不是将 FASTA 文件作为一个整体并以这种方式计算。

from Bio.SeqUtils.ProtParam import ProteinAnalysis 
X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGT" 
                "RDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEEC" 
                "LFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILF" 
                "LPLPV") 
print(X.count_amino_acids()['A']) 
print(X.count_amino_acids()['E']) 
print("%0.2f" % X.get_amino_acids_percent()['K']) 
print("%0.2f" % X.get_amino_acids_percent()['L']) 
print("%0.2f" % X.molecular_weight()) 
print("%0.2f" % X.aromaticity()) 
print("%0.2f" % X.instability_index()) 
print("%0.2f" % X.isoelectric_point()) 
sec_struc = X.secondary_structure_fraction() 
print("%0.2f" % sec_struc[0]) 
epsilon_prot = X.molar_extinction_coefficient()  
print(epsilon_prot[0])   
print(epsilon_prot[1])

Answer 1

您只需要使用 SeqIO.parse():

读取序列的 FASTA 文件

from Bio import SeqIO
from Bio.SeqUtils.ProtParam import ProteinAnalysis

for record in SeqIO.parse('myfasta.fa', 'fasta'):
    X = ProteinAnalysis(str(record.seq))
    print('\n### Results for record: {} ###'.format(record.id))
    print(X.count_amino_acids()['A']) 
    print(X.count_amino_acids()['E']) 
    print("%0.2f" % X.get_amino_acids_percent()['K']) 
    print("%0.2f" % X.get_amino_acids_percent()['L']) 
    print("%0.2f" % X.molecular_weight()) 
    print("%0.2f" % X.aromaticity()) 
    print("%0.2f" % X.instability_index()) 
    print("%0.2f" % X.isoelectric_point()) 
    sec_struc = X.secondary_structure_fraction() 
    print("%0.2f" % sec_struc[0]) 
    epsilon_prot = X.molar_extinction_coefficient()  
    print(epsilon_prot[0])   
    print(epsilon_prot[1])

Answer 2

我认为您需要 FastaIO 模块中的内容，例如：

from Bio.SeqUtils.ProtParam import ProteinAnalysis 
from Bio.SeqIO import FastaIO

with open('myfile.fasta') as fd:
  for name, sequence in FastaIO.SimpleFastaParser(fd):
     X = ProteinAnalysis(sequence)
     print(name, X.count_amino_acids()['A'])

以及你想计算的任何东西

如何计算大型 FASTA 文件中包含的序列的氨基酸组成百分比

How do I calculate percentage amino acid composition of sequences contained in a large FASTA file

python

bioinformatics

biopython

fasta